knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
knitr::opts_chunk$set(echo = F, warning = F, message = F)
Velocyto counts are loaded
## $cluster_res
## [1] 2
##
## $sample_name
## [1] "p014ot0"
##
## $loom_file
## [1] "_data/_patients/velocyto/p014ot0.loom"
##
## $nFeature_lower
## [1] 500
##
## $nFeature_upper
## [1] 5000
##
## $nCount_lower
## [1] 1000
##
## $nCount_upper
## [1] 50000
##
## $nFrac_s_lower
## [1] 0.3
##
## $nFrac_s_upper
## [1] 0.9
##
## $nFrac_u_lower
## [1] 0.1
##
## $nFrac_u_upper
## [1] 0.7
##
## $nFrac_a_lower
## [1] 0
##
## $nFrac_a_upper
## [1] 0.2
##
## $pMT_lower
## [1] 0
##
## $pMT_upper
## [1] 0.8
##
## $pHB_lower
## [1] 0
##
## $pHB_upper
## [1] 0.1
##
## $rel_comp
## [1] 10
## An object of class Seurat
## 100542 features across 21590 samples within 3 assays
## Active assay: spliced (33514 features)
## 2 other assays present: unspliced, ambiguous
## An object of class Seurat
## 100542 features across 18463 samples within 3 assays
## Active assay: spliced (33514 features)
## 2 other assays present: unspliced, ambiguous
| rank | 0 | 1 | 10 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 2 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | NEAT1 | RPS2 | FABP6 | RPS2 | HIST1H4C | TFF1 | HIST1H4C | PHGR1 | CCL20 | CENPF | SPRR3 | FTL | FOS | CXCL1 | LGALS1 | STC1 | GDF15 | KRT19 | TFF1 | FABP1 | PTMA | CCL20 | ||||
| 2 | MALAT1 | RPLP1 | ADIRF | RPLP1 | HMGB2 | REG4 | HIST1H1D | FABP1 | CXCL1 | PTTG1 | KLK10 | S100P | HES1 | CCL20 | VIM | PECAM1 | HLA-A | LGALS4 | FABP1 | PHGR1 | RPS2 | CXCL1 | ||||
| 3 | MUC2 | RPS18 | UGT2B17 | RPS19 | TYMS | KRT8 | UBE2C | LGALS3 | RPS2 | PTMA | REG4 | ADIRF | RPS2 | CXCL3 | IGFBP7 | VIM | MUC13 | FABP1 | PHGR1 | S100A6 | HSP90AB1 | CXCL8 | ||||
| 4 | DDX5 | RPS19 | ANPEP | RPS12 | HIST1H1D | KRT18 | TOP2A | S100A6 | CXCL3 | MKI67 | KRT18 | TPT1 | RPLP1 | CXCL8 | MGP | TCF4 | FTH1 | TXN | S100A6 | LGALS3 | H2AFZ | MUC13 | ||||
| 5 | PLEC | RPS12 | FABP2 | RPS18 | CLSPN | KRT19 | HMGB2 | ADIRF | PTMA | HMGB2 | PI3 | MALAT1 | RPS4X | CXCL2 | SPARC | GNG11 | CEACAM6 | AGR2 | IFI27 | LGALS4 | HMGB1 | TM4SF1 | ||||
| 6 | FAT1 | RPS27 | HSD17B2 | RPL32 | GINS2 | AGR2 | CDK1 | LGALS4 | RPS19 | CCNB1 | CEACAM6 | SPINK1 | RPL3 | NFKBIA | BGN | SPARC | LCN2 | ETHE1 | REG4 | KRT19 | MT1E | SQSTM1 | ||||
| 7 | RPL6 | FXYD3 | RPL3 | HIST1H1B | S100A16 | NUSAP1 | ABCG2 | RPLP1 | HMGB1 | TSPAN8 | MDK | RPS19 | TM4SF1 | CAV1 | SOX18 | SPINK1 | PHLDA2 | TSPAN8 | ANXA10 | RPS19 | AREG | |||||
| 8 | RPL12 | SLC40A1 | RPL13A | HIST1H3B | TFF3 | H2AFZ | KRT20 | RPS6 | HSP90AB1 | GPRC5A | IFI27 | RPS6 | AREG | COL1A2 | CD93 | HLA-C | S100A16 | LGALS3 | S100A10 | RPLP1 | PI3 | |||||
| 9 | AGR2 | SLC26A3 | RPL6 | FAM111B | MUC2 | TYMS | SULT1B1 | RPS18 | DLGAP5 | GSTP1 | SERPINE2 | IER3 | SQSTM1 | FN1 | EGFL7 | SQSTM1 | ANXA10 | ADIRF | KRT8 | MT2A | CLDN3 | |||||
| 10 | RPL3 | MTTP | RPS6 | CENPU | TFF2 | PBK | HPGD | RPS12 | H2AFZ | PLAC8 | HLA-A | RPL23 | CLDN3 | THY1 | RFLNB | TPT1 | AKR1C3 | FXYD3 | KRT20 | TUBA1B | KLK10 | |||||
| 11 | RPL32 | ABCG2 | MT1E | TOP2A | ANXA10 | BIRC5 | AKR1C3 | RPS27 | TOP2A | KLK7 | RPL12 | RPL7A | MUC13 | COL3A1 | MCAM | CD55 | SERPINB1 | LGALS4 | TSPAN8 | RPS6 | PLAC8 | |||||
| 12 | RPL13A | PHGR1 | RPS27 | HIST1H1E | MKI67 | TM4SF4 | RPS4X | NCL | SLPI | SAT1 | RPSA | TMSB4X | COL6A2 | GJA1 | DDIT3 | KRT20 | SERPINB6 | NPM1 | SPRR3 | |||||||
| 13 | RPS14 | FABP1 | RPL10A | BRCA2 | CENPU | MALAT1 | RPS27A | HSP90AA1 | S100A10 | PPDPF | RPS3A | PI3 | CALD1 | COL4A1 | AREG | SLPI | S100A16 | TMSB10 | TSPAN1 | |||||||
| 14 | RPS6 | FTL | RPL12 | TK1 | HMMR | FABP2 | RPL5 | RPS2 | TSPAN1 | MMP1 | RPL10A | GDF15 | PLAC9 | ESM1 | TMSB4X | TM4SF4 | ETHE1 | HSPD1 | MUC2 | |||||||
| 15 | RPS4X | TM4SF4 | RPS14 | GMNN | UBE2T | IFI27 | TMSB10 | NUCKS1 | KRT23 | MYH4 | RPL11 | MUC2 | COL6A3 | PLVAP | PI3 | CEACAM6 | S100A11 | RPL6 | MAL2 | |||||||
| 16 | RPL10A | C10orf99 | RPSA | H2AFZ | TUBA1B | ANPEP | RPS3A | TUBA1B | MAL2 | SLC40A1 | LYZ | IER3 | C11orf96 | TM4SF18 | MALAT1 | TFF2 | DHRS9 | RPS12 | GDF15 | |||||||
| 17 | RPS3A | AKR1B10 | RPLP2 | CDK1 | TUBB | FTL | RPL7A | HSPD1 | AREG | EIF1 | RPL5 | KLK10 | SFRP1 | CRIP2 | SAT1 | HSD17B2 | PHLDA2 | NCL | ||||||||
| 18 | RPL5 | IFI27 | PTMA | PTMA | CENPF | EPCAM | RPS8 | YBX1 | MUC13 | EIF2S2 | PTMA | LCN2 | BEX3 | ADGRF5 | CLDN4 | S100P | SH3BGRL3 | RPL35 | ||||||||
| 19 | RPS8 | PCK1 | RPL13 | HELLS | CKS2 | AKR1B10 | RPL6 | MT1E | CD9 | TMBIM6 | CLDN2 | TCEAL9 | KDR | HLA-E | AKR1B10 | AKR1C3 | YBX1 | |||||||||
| 20 | RPSA | SULT1B1 | RPS27A | MAD2L1 | PTMA | SLC22A18 | RPL13A | NPM1 | LGALS3 | ZFAS1 | RPS8 | GNG11 | A2M | TSPAN1 | HPGD | CD9 | NASP | |||||||||
| 21 | RPLP2 | SMIM24 | RPL21 | TUBA1B | HMGB1 | TMEM54 | RPL10A | ANP32B | SH3BGRL3 | FTH1 | RPS12 | CYGB | CLEC14A | TMC5 | CTSE | SERPINB1 | LDHB | |||||||||
| 22 | RPS3 | HPGD | TMSB10 | PCNA | PCNA | ETHE1 | RPL3 | CKS2 | CD55 | SYF2 | RPS27A | COL18A1 | CLDN5 | UBC | SH3BGRL3 | GUCA2A | RPSA | |||||||||
| 23 | RPLP0 | LGALS4 | RPS16 | MKI67 | MAD2L1 | SRI | RPSA | SERBP1 | ADGRF1 | TMEM59 | RPL13A | PDGFRB | CLEC2B | RAB11FIP1 | TFF3 | REG4 | ANP32B | |||||||||
| 24 | RPL21 | AKR1C3 | RPS3 | UBE2T | RANBP1 | CXCL8 | LDHB | TM4SF4 | CAMK2N1 | RPS3 | MCAM | PXDN | MUC2 | SLC22A18 | KRT18 | PTTG1 | ||||||||||
| 25 | RPS9 | C2orf88 | RPS3A | RAD51AP1 | PTTG1 | RPS15A | HNRNPM | KLK6 | HLA-C | RPS27 | COX7A1 | FLT1 | ABHD2 | EPCAM | S100A14 | RPS27A | ||||||||||
| 26 | C3orf85 | RPS4X | NASP | DTYMK | NPM1 | HNRNPAB | TM4SF1 | LCN2 | NAP1L1 | ANTXR1 | ENG | KLK10 | SMIM22 | TXNDC17 | RPS18 | |||||||||||
| 27 | SLC51B | RPS8 | DUT | DUT | YBX1 | PTGES3 | CLDN3 | RPS7 | MAP1B | ACKR3 | JUN | ANXA10 | TMEM54 | RPS27 | ||||||||||||
| 28 | MEP1A | RPS7 | RFC3 | NASP | RPL35A | SRSF3 | CLIC1 | DUSP1 | NOTCH3 | SPARCL1 | CLDN3 | ISG20 | ABCG2 | RPL10A | ||||||||||||
| 29 | CBR1 | RPL35 | HMGB1 | RPA3 | LDHB | HNRNPA2B1 | ANXA3 | RPL13 | SERPINE1 | GIMAP4 | OCIAD2 | MMP1 | HPGD | RPL5 | ||||||||||||
| 30 | LGALS3 | RPL19 | PBK | KPNA2 | RPS5 | ENO1 | TMC5 | LDHB | EMP3 | CDH5 | FOS | DHRS9 | JPT1 | RPL13A | ||||||||||||
| 31 | PSCA | RPLP0 | UBE2C | MT2A | MT1E | DEK | EPCAM | AQP5 | TUBA1A | GIMAP7 | IER2 | RHOC | ARL14 | RPL3 | ||||||||||||
| 32 | CD36 | RPL37 | CENPM | MT1E | RPL23 | RAN | SFN | ID3 | PLAU | RDX | MMP1 | CAMK2N1 | ISG20 | RPS4X | ||||||||||||
| 33 | CEACAM7 | RPL5 | MCM6 | NUCKS1 | H2AFZ | RPL22L1 | DHRS9 | EGR1 | CCDC102B | CALCRL | SCD | ATP2B1 | ENO1 | |||||||||||||
| 34 | ITM2B | NACA | MCM7 | H1FX | NAP1L1 | NAP1L1 | KRT20 | GDF15 | PLAT | IQCA1 | SERPINB6 | TM4SF4 | NUCKS1 | |||||||||||||
| 35 | DHRS11 | GAPDH | ZWINT | LDHB | RPLP0 | TUBB | MUC2 | YBX1 | COL6A1 | CYTL1 | MGST3 | GMNN | ||||||||||||||
| 36 | TSPAN8 | RPL11 | BIRC5 | DEK | RPS3 | CLDN4 | RPL6 | STC1 | TNFRSF4 | SLC9A3R1 | GAPDH | |||||||||||||||
| 37 | UQCRQ | RPL7A | MT2A | SNRPG | MT2A | ABHD2 | RPS5 | SELENOM | PCDH17 | DNAJC15 | HSP90AA1 | |||||||||||||||
| 38 | S100A6 | RPL36 | TUBB | RAN | PKM | TFF2 | TSC22D1 | TAGLN | EMCN | DSC2 | RPL32 | |||||||||||||||
| 39 | CAMK2N1 | RPL35A | NUSAP1 | TUBB4B | HSP90AB1 | LMO7 | JUN | COL1A1 | TCEAL4 | RANBP1 | ||||||||||||||||
| 40 | TXNIP | RPS24 | RRM1 | NPM1 | HIST1H4C | LMO4 | RPS15A | SPON2 | NBDY | RPS3 | ||||||||||||||||
| 41 | SRI | RPS5 | MT1E | HNRNPDL | HMGB1 | SLC12A2 | ACTA2 | HEY1 | RPS5 | |||||||||||||||||
| 42 | OAT | RPS15A | RANBP1 | HSPD1 | RPL21 | MT1E | NR2F1 | ADAMTS1 | RPLP2 | |||||||||||||||||
| 43 | CES2 | RPL18A | RPS2 | SRSF3 | ENO1 | RPS9 | IFITM3 | CAV1 | RPL7A | |||||||||||||||||
| 44 | DHRS7 | HMGB1 | PTTG1 | RPL22L1 | RPL22L1 | IL33 | CAVIN3 | ANGPT2 | RPL19 | |||||||||||||||||
| 45 | CTSE | RPL23 | DNMT1 | SNRPF | SLC25A6 | RPL4 | TIMP1 | CXCR4 | RPS16 | |||||||||||||||||
| 46 | COX6C | NPM1 | LDHB | HNRNPAB | NUCKS1 | IER2 | COL4A2 | RGCC | RAN | |||||||||||||||||
| 47 | GHITM | HSP90AB1 | DTYMK | NCL | SNRPD2 | PKM | TMEM158 | BEX3 | RPL22L1 | |||||||||||||||||
| 48 | CDHR5 | RPL28 | NPM1 | ANP32B | SNRPF | ID1 | MFGE8 | MEF2C | NAP1L1 | |||||||||||||||||
| 49 | CEACAM6 | RPL34 | CENPF | NAP1L1 | TUBA1B | RPL22L1 | NR2F2 | LGALS1 | RPS3A | |||||||||||||||||
| 50 | ALDH1A1 | RPS29 | YBX1 | IER3 | LCN2 | TFPI | NRP1 | SNRPF | ||||||||||||||||||
| 51 | SPPL2A | RPL8 | BTG3 | KANK2 | WWTR1 | RPL8 | ||||||||||||||||||||
| 52 | AOC1 | RPL37A | SMC2 | TPM2 | ELK3 | PCNA | ||||||||||||||||||||
| 53 | MALAT1 | RPL23A | MCM3 | S100A4 | FAM198B | RPL23A | ||||||||||||||||||||
| 54 | COX7B | RPS28 | H2AFX | RARRES2 | HTRA1 | RPL23 | ||||||||||||||||||||
| 55 | CRYL1 | RPS23 | TPX2 | ZFP36L1 | IGFBP3 | RPL13 | ||||||||||||||||||||
| 56 | ATP1B1 | LDHB | KIF20B | CD81 | COL4A2 | RPS7 | ||||||||||||||||||||
| 57 | HSPB1 | RPS20 | ANP32B | ANXA5 | IFITM3 | RPL36 | ||||||||||||||||||||
| 58 | FAM213A | YBX1 | NCL | MT2A | BCAM | SERBP1 | ||||||||||||||||||||
| 59 | PRR15 | MT2A | NUCKS1 | ID4 | CTGF | RPL21 | ||||||||||||||||||||
| 60 | SLC22A18 | RPL24 | USP1 | TLN1 | PGM2L1 | RPS15A | ||||||||||||||||||||
| 61 | CA2 | RPL10 | NAP1L1 | CD63 | CAVIN1 | RPL35A | ||||||||||||||||||||
| 62 | GUCA2A | NAP1L1 | PSIP1 | DSTN | FABP5 | RPS23 | ||||||||||||||||||||
| 63 | GPA33 | RPS11 | DEK | ITGB1 | ARRDC3 | RPS20 | ||||||||||||||||||||
| 64 | EPCAM | RPS15 | RPS19 | IGFBP2 | SPRY1 | RPS15 | ||||||||||||||||||||
| 65 | SAT1 | RPL27 | HSPD1 | PNRC1 | NDST1 | RPL18A | ||||||||||||||||||||
| 66 | DUSP1 | AGR2 | HSP90AB1 | TUBA1B | INSR | SNHG19 | ||||||||||||||||||||
| 67 | NDUFA1 | RPL31 | TMSB10 | ID3 | PLK2 | RPLP0 | ||||||||||||||||||||
| 68 | SELENOW | RPL30 | CDK4 | CEBPB | CAV2 | HNRNPM | ||||||||||||||||||||
| 69 | SMIM22 | ENO1 | RAN | EID1 | CDC42EP3 | NACA | ||||||||||||||||||||
| 70 | CDH17 | RPS9 | SMC4 | MARCKS | LAMC1 | CENPF | ||||||||||||||||||||
| 71 | PRR13 | RPL18 | SNRPF | EPS8 | UNC5B | DEK | ||||||||||||||||||||
| 72 | FUOM | EEF1B2 | ENO1 | HLA-E | RPL27 | |||||||||||||||||||||
| 73 | SCP2 | RPL22L1 | FBL | CYR61 | HNRNPA2B1 | |||||||||||||||||||||
| 74 | PRDX6 | HSPD1 | RPLP1 | HLA-C | SNRPD1 | |||||||||||||||||||||
| 75 | JUN | NCL | AQP5 | IVNS1ABP | PKM | |||||||||||||||||||||
| 76 | LIMA1 | RPL7 | RPS6 | HLA-A | HSPE1 | |||||||||||||||||||||
| 77 | SLPI | RPL22 | H1FX | ITM2B | SNRPG | |||||||||||||||||||||
| 78 | MGST3 | H2AFZ | RPSA | POMP | RPL7 | |||||||||||||||||||||
| 79 | TST | SNRPD2 | RPS3A | EFNA1 | SET | |||||||||||||||||||||
| 80 | ECHS1 | SERBP1 | RPS4X | ARHGAP29 | HNRNPDL | |||||||||||||||||||||
| 81 | PIGR | MT1G | EZH2 | CD81 | EEF1B2 | |||||||||||||||||||||
| 82 | ANP32B | SIVA1 | SPTBN1 | SRSF3 | ||||||||||||||||||||||
| 83 | NUCKS1 | HSP90AA1 | YBX3 | PTGES3 | ||||||||||||||||||||||
| 84 | SNRPF | RPL22L1 | SH3BP5 | MT1G | ||||||||||||||||||||||
| 85 | GAPDH | SNX3 | RPS9 | |||||||||||||||||||||||
| 86 | RPA3 | TMSB4X | SNRPD2 | |||||||||||||||||||||||
| 87 | DBF4 | EMP1 | RPL4 | |||||||||||||||||||||||
| 88 | SUPT16H | JAK1 | NAA38 | |||||||||||||||||||||||
| 89 | SRSF3 | BTG1 | HNRNPAB | |||||||||||||||||||||||
| 90 | RPS27A | CALM1 | RPL22 | |||||||||||||||||||||||
| 91 | SNRPD1 | FOSB | TUBB | |||||||||||||||||||||||
| 92 | RPS3 | SMAD1 | HMGN1 | |||||||||||||||||||||||
| 93 | RPL5 | TSC22D1 | SRSF7 | |||||||||||||||||||||||
| 94 | RPS12 | ARHGAP18 | LSM7 | |||||||||||||||||||||||
| 95 | RPS8 | PPP1R15A | HMGA1 | |||||||||||||||||||||||
| 96 | SERBP1 | ETS2 | SLC25A6 | |||||||||||||||||||||||
| 97 | PAICS | XPC | LSM5 | |||||||||||||||||||||||
| 98 | HNRNPD | B2M | HNRNPK | |||||||||||||||||||||||
| 99 | RPL35 | DARS | EIF5A | |||||||||||||||||||||||
| 100 | SNRPG | MYO10 | C1QBP | |||||||||||||||||||||||
| NA | no_sig_genes | no_sig_genes | no_sig_genes | no_sig_genes |